Nucleic acid analysis in a sample has many applications in both basic research and clinical settings. For example, nucleic acid analysis may be used to identify genetic aberrations in a patient blood sample. Genetic aberrations account for a large number of pathological conditions, including syndromic disorders (e.g., Down's syndrome) and diseases (e.g., breast cancer). Genetic aberrations may be, but is not limited to, single nucleotide polymorphisms (SNPs), gene copy number variants (CNVs), chromosomal rearrangements (e.g., insertions, deletions and duplications), gene mutations (e.g., single nucleotide changes, insertions, and deletions), nucleic acid modifications (e.g., methylation, acetylation and phosphorylations), gene over-expression (e.g., an oncogenes such as RAS), and gene under-expression (e.g., a tumor suppressor gene such as p53). In addition, nucleic acid analysis may be used to identify pathogens and transgenic organisms.
Many techniques have been developed for nucleic acid analysis. For one example, techniques such as oligonucleotide ligation assay (OLA) and ligation chain reaction (LCR) have been used to detect SNPs. See, e.g., Abravaya, et al., 1995, Detection of point mutations with a modified ligase chain reaction (Gap-LCR), Nucleic Acids Res. 23:675-82; Landegren et al., 1988, A ligase-mediated gene detection technique, Science. 241:1077-80; Schwartz et al., 2009, Identification of cystic fibrosis variants by polymerase chain reaction/oligonucleotide ligation assay, J Mol Diagn. 11:211-5. For another example, microarrays and high throughput DNA sequencing may be used to detect chromosome rearrangements and gene copy numbers. See, e.g., Agilent Human Genome CGH Microarray (Agilent Technologies, Inc., Santa Clara, Calif.), and the Illumina HiSeq DNA Sequencing Assays (Illumina, Inc., San Diego, Calif.). However, the nucleic acid analysis using these known techniques are either not easily multiplexed (e.g., the OLA and LCR methods), or time-consuming, expensive and/or inaccurate (e.g., microarrays and high throughput DNA sequencing).
Therefore, it is desirable to have a new technique that makes the nucleic acid analysis easily multiplexed and efficient. An object of the present invention is to provide methods and kits for multiplexed and efficient nucleic acid analysis in a sample. The methods and kits based on the present invention may be suitable for adaptation and incorporation into a compact device or instrument for use in a laboratory or a clinical setting, or in the field.
No reference cited in this background section is to be construed as an “admission” of prior art. Applicant expressly reserves the right to demonstrate, where appropriate, that the references cited herein do not constitute prior art under the applicable statutory provisions.